Starting phenix.real_space_refine on Sun Jun 15 02:26:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8frw_29409/06_2025/8frw_29409.cif Found real_map, /net/cci-nas-00/data/ceres_data/8frw_29409/06_2025/8frw_29409.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8frw_29409/06_2025/8frw_29409.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8frw_29409/06_2025/8frw_29409.map" model { file = "/net/cci-nas-00/data/ceres_data/8frw_29409/06_2025/8frw_29409.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8frw_29409/06_2025/8frw_29409.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 10990 2.51 5 N 2705 2.21 5 O 2935 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16680 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3270 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Chain: "B" Number of atoms: 3270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3270 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 65 Unusual residues: {'NAG': 3, 'Y7H': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 65 Unusual residues: {'NAG': 3, 'Y7H': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Restraints were copied for chains: C, D, E Time building chain proxies: 9.42, per 1000 atoms: 0.56 Number of scatterers: 16680 At special positions: 0 Unit cell: (95.7, 96.8, 171.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 2935 8.00 N 2705 7.00 C 10990 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 149 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 82 " " NAG A 502 " - " ASN A 148 " " NAG A 503 " - " ASN A 164 " " NAG B 502 " - " ASN B 82 " " NAG B 503 " - " ASN B 148 " " NAG B 504 " - " ASN B 164 " " NAG C 502 " - " ASN C 82 " " NAG C 503 " - " ASN C 148 " " NAG C 504 " - " ASN C 164 " " NAG D 502 " - " ASN D 82 " " NAG D 503 " - " ASN D 148 " " NAG D 504 " - " ASN D 164 " " NAG E 502 " - " ASN E 82 " " NAG E 503 " - " ASN E 148 " " NAG E 504 " - " ASN E 164 " Time building additional restraints: 3.73 Conformation dependent library (CDL) restraints added in 2.0 seconds 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3840 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 15 sheets defined 43.5% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 10 through 21 removed outlier: 3.682A pdb=" N SER A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 170 through 175 Processing helix chain 'A' and resid 220 through 243 removed outlier: 4.001A pdb=" N VAL A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 250 through 270 Processing helix chain 'A' and resid 281 through 309 removed outlier: 3.868A pdb=" N VAL A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 328 removed outlier: 3.683A pdb=" N LEU A 321 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N HIS A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 462 removed outlier: 3.695A pdb=" N ILE A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 21 removed outlier: 3.681A pdb=" N SER B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 170 through 175 Processing helix chain 'B' and resid 220 through 243 removed outlier: 4.002A pdb=" N VAL B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 250 through 270 Processing helix chain 'B' and resid 281 through 309 removed outlier: 3.868A pdb=" N VAL B 285 " --> pdb=" O PRO B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 328 removed outlier: 3.682A pdb=" N LEU B 321 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N HIS B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 325 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 462 removed outlier: 3.694A pdb=" N ILE B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 21 removed outlier: 3.681A pdb=" N SER C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 170 through 175 Processing helix chain 'C' and resid 220 through 243 removed outlier: 4.001A pdb=" N VAL C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Proline residue: C 230 - end of helix Processing helix chain 'C' and resid 250 through 270 Processing helix chain 'C' and resid 281 through 309 removed outlier: 3.868A pdb=" N VAL C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 328 removed outlier: 3.682A pdb=" N LEU C 321 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N HIS C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL C 325 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU C 326 " --> pdb=" O ARG C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 462 removed outlier: 3.695A pdb=" N ILE C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 21 removed outlier: 3.682A pdb=" N SER D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 170 through 175 Processing helix chain 'D' and resid 220 through 243 removed outlier: 4.002A pdb=" N VAL D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) Proline residue: D 230 - end of helix Processing helix chain 'D' and resid 250 through 270 Processing helix chain 'D' and resid 281 through 309 removed outlier: 3.869A pdb=" N VAL D 285 " --> pdb=" O PRO D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 328 removed outlier: 3.682A pdb=" N LEU D 321 " --> pdb=" O VAL D 317 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N HIS D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL D 325 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 462 removed outlier: 3.695A pdb=" N ILE D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 21 removed outlier: 3.681A pdb=" N SER E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 170 through 175 Processing helix chain 'E' and resid 220 through 243 removed outlier: 4.003A pdb=" N VAL E 225 " --> pdb=" O LEU E 221 " (cutoff:3.500A) Proline residue: E 230 - end of helix Processing helix chain 'E' and resid 250 through 270 Processing helix chain 'E' and resid 281 through 309 removed outlier: 3.868A pdb=" N VAL E 285 " --> pdb=" O PRO E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 328 removed outlier: 3.682A pdb=" N LEU E 321 " --> pdb=" O VAL E 317 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N HIS E 323 " --> pdb=" O ASP E 319 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL E 325 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU E 326 " --> pdb=" O ARG E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 462 removed outlier: 3.694A pdb=" N ILE E 409 " --> pdb=" O GLU E 405 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 89 removed outlier: 7.313A pdb=" N TYR A 114 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR A 126 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL A 132 " --> pdb=" O VAL A 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 89 removed outlier: 7.313A pdb=" N TYR A 114 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR A 126 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY A 121 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N TYR A 61 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE A 48 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N TRP A 63 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N TYR A 46 " --> pdb=" O TRP A 63 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ARG A 65 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE A 44 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N TYR A 67 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ASP A 42 " --> pdb=" O TYR A 67 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N THR A 69 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 9.666A pdb=" N SER A 40 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 10.088A pdb=" N GLU A 71 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 13.372A pdb=" N THR A 38 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR A 37 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N THR A 166 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL A 39 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.495A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TYR A 207 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLU A 198 " --> pdb=" O TYR A 207 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLU A 209 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N PHE A 196 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS A 211 " --> pdb=" O PRO A 194 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N TYR A 213 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL A 192 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE A 215 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 85 through 89 removed outlier: 7.312A pdb=" N TYR B 114 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TYR B 126 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU B 122 " --> pdb=" O HIS B 118 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL B 132 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 85 through 89 removed outlier: 7.312A pdb=" N TYR B 114 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TYR B 126 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU B 122 " --> pdb=" O HIS B 118 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY B 121 " --> pdb=" O ASP B 70 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR B 61 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE B 48 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N TRP B 63 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TYR B 46 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ARG B 65 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE B 44 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N TYR B 67 " --> pdb=" O ASP B 42 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ASP B 42 " --> pdb=" O TYR B 67 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N THR B 69 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 9.666A pdb=" N SER B 40 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N GLU B 71 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 13.373A pdb=" N THR B 38 " --> pdb=" O GLU B 71 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR B 37 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N THR B 166 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL B 39 " --> pdb=" O THR B 166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.496A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N TYR B 207 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLU B 198 " --> pdb=" O TYR B 207 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLU B 209 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N PHE B 196 " --> pdb=" O GLU B 209 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS B 211 " --> pdb=" O PRO B 194 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N TYR B 213 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL B 192 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE B 215 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 85 through 89 removed outlier: 7.312A pdb=" N TYR C 114 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR C 126 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N VAL C 132 " --> pdb=" O VAL C 104 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 85 through 89 removed outlier: 7.312A pdb=" N TYR C 114 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR C 126 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY C 121 " --> pdb=" O ASP C 70 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TYR C 61 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE C 48 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N TRP C 63 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TYR C 46 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ARG C 65 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE C 44 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N TYR C 67 " --> pdb=" O ASP C 42 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ASP C 42 " --> pdb=" O TYR C 67 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N THR C 69 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 9.666A pdb=" N SER C 40 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 10.087A pdb=" N GLU C 71 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 13.372A pdb=" N THR C 38 " --> pdb=" O GLU C 71 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR C 37 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N THR C 166 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL C 39 " --> pdb=" O THR C 166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.496A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N TYR C 207 " --> pdb=" O GLU C 198 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLU C 198 " --> pdb=" O TYR C 207 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLU C 209 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N PHE C 196 " --> pdb=" O GLU C 209 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LYS C 211 " --> pdb=" O PRO C 194 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N TYR C 213 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL C 192 " --> pdb=" O TYR C 213 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE C 215 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 85 through 89 removed outlier: 7.312A pdb=" N TYR D 114 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR D 126 " --> pdb=" O TYR D 114 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL D 132 " --> pdb=" O VAL D 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 85 through 89 removed outlier: 7.312A pdb=" N TYR D 114 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR D 126 " --> pdb=" O TYR D 114 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY D 121 " --> pdb=" O ASP D 70 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TYR D 61 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE D 48 " --> pdb=" O TYR D 61 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N TRP D 63 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N TYR D 46 " --> pdb=" O TRP D 63 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ARG D 65 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ILE D 44 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N TYR D 67 " --> pdb=" O ASP D 42 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ASP D 42 " --> pdb=" O TYR D 67 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N THR D 69 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 9.665A pdb=" N SER D 40 " --> pdb=" O THR D 69 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N GLU D 71 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 13.373A pdb=" N THR D 38 " --> pdb=" O GLU D 71 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR D 37 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N THR D 166 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL D 39 " --> pdb=" O THR D 166 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.496A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N TYR D 207 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLU D 198 " --> pdb=" O TYR D 207 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLU D 209 " --> pdb=" O PHE D 196 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N PHE D 196 " --> pdb=" O GLU D 209 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS D 211 " --> pdb=" O PRO D 194 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N TYR D 213 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL D 192 " --> pdb=" O TYR D 213 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE D 215 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 85 through 89 removed outlier: 7.312A pdb=" N TYR E 114 " --> pdb=" O TYR E 126 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TYR E 126 " --> pdb=" O TYR E 114 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU E 122 " --> pdb=" O HIS E 118 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL E 132 " --> pdb=" O VAL E 104 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 85 through 89 removed outlier: 7.312A pdb=" N TYR E 114 " --> pdb=" O TYR E 126 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TYR E 126 " --> pdb=" O TYR E 114 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU E 122 " --> pdb=" O HIS E 118 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLY E 121 " --> pdb=" O ASP E 70 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TYR E 61 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE E 48 " --> pdb=" O TYR E 61 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N TRP E 63 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TYR E 46 " --> pdb=" O TRP E 63 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ARG E 65 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE E 44 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N TYR E 67 " --> pdb=" O ASP E 42 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ASP E 42 " --> pdb=" O TYR E 67 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N THR E 69 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 9.666A pdb=" N SER E 40 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N GLU E 71 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 13.373A pdb=" N THR E 38 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR E 37 " --> pdb=" O ASN E 164 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N THR E 166 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL E 39 " --> pdb=" O THR E 166 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.495A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N TYR E 207 " --> pdb=" O GLU E 198 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLU E 198 " --> pdb=" O TYR E 207 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLU E 209 " --> pdb=" O PHE E 196 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N PHE E 196 " --> pdb=" O GLU E 209 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LYS E 211 " --> pdb=" O PRO E 194 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N TYR E 213 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL E 192 " --> pdb=" O TYR E 213 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE E 215 " --> pdb=" O LEU E 190 " (cutoff:3.500A) 875 hydrogen bonds defined for protein. 2610 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.95 Time building geometry restraints manager: 4.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2550 1.32 - 1.44: 4900 1.44 - 1.57: 9620 1.57 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 17145 Sorted by residual: bond pdb=" C16 Y7H A 504 " pdb=" C17 Y7H A 504 " ideal model delta sigma weight residual 1.559 1.492 0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C16 Y7H B 501 " pdb=" C17 Y7H B 501 " ideal model delta sigma weight residual 1.559 1.492 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C16 Y7H E 501 " pdb=" C17 Y7H E 501 " ideal model delta sigma weight residual 1.559 1.493 0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" C16 Y7H D 501 " pdb=" C17 Y7H D 501 " ideal model delta sigma weight residual 1.559 1.493 0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C16 Y7H C 501 " pdb=" C17 Y7H C 501 " ideal model delta sigma weight residual 1.559 1.493 0.066 2.00e-02 2.50e+03 1.07e+01 ... (remaining 17140 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 22777 2.03 - 4.07: 521 4.07 - 6.10: 102 6.10 - 8.13: 25 8.13 - 10.17: 15 Bond angle restraints: 23440 Sorted by residual: angle pdb=" N ILE C 203 " pdb=" CA ILE C 203 " pdb=" C ILE C 203 " ideal model delta sigma weight residual 112.80 104.12 8.68 1.15e+00 7.56e-01 5.69e+01 angle pdb=" N ILE D 203 " pdb=" CA ILE D 203 " pdb=" C ILE D 203 " ideal model delta sigma weight residual 112.80 104.14 8.66 1.15e+00 7.56e-01 5.67e+01 angle pdb=" N ILE B 203 " pdb=" CA ILE B 203 " pdb=" C ILE B 203 " ideal model delta sigma weight residual 112.80 104.15 8.65 1.15e+00 7.56e-01 5.66e+01 angle pdb=" N ILE E 203 " pdb=" CA ILE E 203 " pdb=" C ILE E 203 " ideal model delta sigma weight residual 112.80 104.18 8.62 1.15e+00 7.56e-01 5.61e+01 angle pdb=" N ILE A 203 " pdb=" CA ILE A 203 " pdb=" C ILE A 203 " ideal model delta sigma weight residual 112.80 104.19 8.61 1.15e+00 7.56e-01 5.61e+01 ... (remaining 23435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 9364 17.49 - 34.97: 837 34.97 - 52.46: 154 52.46 - 69.95: 20 69.95 - 87.43: 5 Dihedral angle restraints: 10380 sinusoidal: 4485 harmonic: 5895 Sorted by residual: dihedral pdb=" CA ILE B 163 " pdb=" C ILE B 163 " pdb=" N ASN B 164 " pdb=" CA ASN B 164 " ideal model delta harmonic sigma weight residual 180.00 157.53 22.47 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA ILE D 163 " pdb=" C ILE D 163 " pdb=" N ASN D 164 " pdb=" CA ASN D 164 " ideal model delta harmonic sigma weight residual 180.00 157.58 22.42 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA ILE A 163 " pdb=" C ILE A 163 " pdb=" N ASN A 164 " pdb=" CA ASN A 164 " ideal model delta harmonic sigma weight residual 180.00 157.59 22.41 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 10377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1884 0.039 - 0.077: 569 0.077 - 0.116: 216 0.116 - 0.155: 68 0.155 - 0.193: 18 Chirality restraints: 2755 Sorted by residual: chirality pdb=" C1 NAG B 502 " pdb=" ND2 ASN B 82 " pdb=" C2 NAG B 502 " pdb=" O5 NAG B 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.33e-01 chirality pdb=" CA ILE C 203 " pdb=" N ILE C 203 " pdb=" C ILE C 203 " pdb=" CB ILE C 203 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.09e-01 chirality pdb=" C1 NAG A 501 " pdb=" ND2 ASN A 82 " pdb=" C2 NAG A 501 " pdb=" O5 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.05e-01 ... (remaining 2752 not shown) Planarity restraints: 2855 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 44 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.13e+00 pdb=" C ILE A 44 " 0.052 2.00e-02 2.50e+03 pdb=" O ILE A 44 " -0.020 2.00e-02 2.50e+03 pdb=" N MET A 45 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 44 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.04e+00 pdb=" C ILE C 44 " 0.052 2.00e-02 2.50e+03 pdb=" O ILE C 44 " -0.019 2.00e-02 2.50e+03 pdb=" N MET C 45 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 44 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.04e+00 pdb=" C ILE B 44 " 0.052 2.00e-02 2.50e+03 pdb=" O ILE B 44 " -0.019 2.00e-02 2.50e+03 pdb=" N MET B 45 " -0.017 2.00e-02 2.50e+03 ... (remaining 2852 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4678 2.83 - 3.35: 15365 3.35 - 3.86: 27578 3.86 - 4.38: 29713 4.38 - 4.90: 52128 Nonbonded interactions: 129462 Sorted by model distance: nonbonded pdb=" OH TYR C 64 " pdb=" OE1 GLN C 66 " model vdw 2.312 3.040 nonbonded pdb=" OH TYR A 64 " pdb=" OE1 GLN A 66 " model vdw 2.312 3.040 nonbonded pdb=" OH TYR E 64 " pdb=" OE1 GLN E 66 " model vdw 2.312 3.040 nonbonded pdb=" OH TYR B 64 " pdb=" OE1 GLN B 66 " model vdw 2.312 3.040 nonbonded pdb=" OH TYR D 64 " pdb=" OE1 GLN D 66 " model vdw 2.312 3.040 ... (remaining 129457 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 462 or resid 502 through 503)) selection = (chain 'B' and (resid 7 through 462 or resid 502 through 503)) selection = (chain 'C' and (resid 7 through 462 or resid 502 through 503)) selection = (chain 'D' and (resid 7 through 462 or resid 502 through 503)) selection = (chain 'E' and (resid 7 through 462 or resid 502 through 503)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 35.760 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 17165 Z= 0.239 Angle : 0.792 10.168 23495 Z= 0.413 Chirality : 0.048 0.193 2755 Planarity : 0.005 0.038 2840 Dihedral : 13.230 87.432 6525 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.11 % Allowed : 0.98 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.19), residues: 1955 helix: 2.24 (0.19), residues: 735 sheet: -0.03 (0.26), residues: 355 loop : -0.86 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 320 HIS 0.003 0.001 HIS E 323 PHE 0.017 0.002 PHE B 233 TYR 0.016 0.001 TYR B 67 ARG 0.007 0.000 ARG D 424 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 15) link_NAG-ASN : angle 4.55208 ( 45) hydrogen bonds : bond 0.11774 ( 840) hydrogen bonds : angle 4.95822 ( 2610) SS BOND : bond 0.00105 ( 5) SS BOND : angle 0.51733 ( 10) covalent geometry : bond 0.00464 (17145) covalent geometry : angle 0.76744 (23440) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 159 time to evaluate : 1.938 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 159 average time/residue: 0.9755 time to fit residues: 179.3000 Evaluate side-chains 65 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.0070 chunk 147 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.089128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.062341 restraints weight = 41818.597| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.86 r_work: 0.2882 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17165 Z= 0.115 Angle : 0.552 6.886 23495 Z= 0.273 Chirality : 0.042 0.144 2755 Planarity : 0.004 0.035 2840 Dihedral : 5.152 34.821 2645 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.19 % Allowed : 7.37 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.20), residues: 1955 helix: 2.29 (0.19), residues: 770 sheet: 0.03 (0.28), residues: 330 loop : -0.67 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 459 HIS 0.002 0.000 HIS A 323 PHE 0.005 0.001 PHE A 254 TYR 0.013 0.001 TYR C 67 ARG 0.003 0.000 ARG A 424 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 15) link_NAG-ASN : angle 2.46056 ( 45) hydrogen bonds : bond 0.04162 ( 840) hydrogen bonds : angle 3.95215 ( 2610) SS BOND : bond 0.00306 ( 5) SS BOND : angle 0.57208 ( 10) covalent geometry : bond 0.00247 (17145) covalent geometry : angle 0.54182 (23440) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 1.704 Fit side-chains revert: symmetry clash REVERT: A 267 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8464 (tp) REVERT: C 242 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.8135 (t80) REVERT: D 267 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8562 (tp) REVERT: E 54 LYS cc_start: 0.8937 (pttm) cc_final: 0.8725 (pmtt) REVERT: E 267 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8480 (tp) outliers start: 22 outliers final: 9 residues processed: 96 average time/residue: 0.8856 time to fit residues: 100.1217 Evaluate side-chains 76 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 7 optimal weight: 0.0040 chunk 42 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 chunk 179 optimal weight: 0.5980 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.087221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.059934 restraints weight = 41345.523| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.84 r_work: 0.2813 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17165 Z= 0.114 Angle : 0.521 7.602 23495 Z= 0.257 Chirality : 0.042 0.132 2755 Planarity : 0.003 0.033 2840 Dihedral : 4.500 26.632 2645 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.30 % Allowed : 8.78 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.20), residues: 1955 helix: 2.38 (0.19), residues: 800 sheet: -0.04 (0.27), residues: 330 loop : -0.72 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 320 HIS 0.002 0.001 HIS C 323 PHE 0.010 0.001 PHE C 233 TYR 0.018 0.001 TYR E 116 ARG 0.008 0.000 ARG E 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 15) link_NAG-ASN : angle 2.57322 ( 45) hydrogen bonds : bond 0.04287 ( 840) hydrogen bonds : angle 3.77959 ( 2610) SS BOND : bond 0.00359 ( 5) SS BOND : angle 0.62638 ( 10) covalent geometry : bond 0.00249 (17145) covalent geometry : angle 0.50962 (23440) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 1.898 Fit side-chains REVERT: A 267 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8477 (tp) REVERT: B 267 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8609 (tp) REVERT: C 267 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8460 (tp) REVERT: D 267 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8562 (tp) REVERT: E 54 LYS cc_start: 0.8908 (pttm) cc_final: 0.8686 (pmtt) REVERT: E 235 MET cc_start: 0.8775 (mmm) cc_final: 0.8481 (mmm) REVERT: E 267 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8496 (tp) outliers start: 24 outliers final: 3 residues processed: 95 average time/residue: 0.9906 time to fit residues: 109.6273 Evaluate side-chains 71 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain E residue 267 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 90 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 151 optimal weight: 0.7980 chunk 179 optimal weight: 6.9990 chunk 133 optimal weight: 0.0570 chunk 74 optimal weight: 1.9990 chunk 10 optimal weight: 0.0670 chunk 81 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.086087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.058996 restraints weight = 41495.618| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.83 r_work: 0.2794 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17165 Z= 0.113 Angle : 0.510 6.235 23495 Z= 0.252 Chirality : 0.041 0.128 2755 Planarity : 0.003 0.033 2840 Dihedral : 4.414 25.330 2645 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.08 % Allowed : 10.84 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.20), residues: 1955 helix: 2.48 (0.19), residues: 795 sheet: -0.02 (0.27), residues: 330 loop : -0.66 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 320 HIS 0.002 0.001 HIS A 309 PHE 0.008 0.001 PHE A 242 TYR 0.015 0.001 TYR C 67 ARG 0.001 0.000 ARG C 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00253 ( 15) link_NAG-ASN : angle 2.50890 ( 45) hydrogen bonds : bond 0.04230 ( 840) hydrogen bonds : angle 3.77157 ( 2610) SS BOND : bond 0.00340 ( 5) SS BOND : angle 0.61912 ( 10) covalent geometry : bond 0.00254 (17145) covalent geometry : angle 0.49850 (23440) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 1.794 Fit side-chains REVERT: A 267 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8462 (tp) REVERT: B 267 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8604 (tp) REVERT: C 267 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8483 (tp) REVERT: D 267 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8564 (tp) REVERT: E 54 LYS cc_start: 0.8922 (pttm) cc_final: 0.8699 (pmtt) REVERT: E 235 MET cc_start: 0.8778 (mmm) cc_final: 0.8461 (mmm) REVERT: E 267 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8483 (tp) outliers start: 20 outliers final: 7 residues processed: 92 average time/residue: 0.9585 time to fit residues: 102.7222 Evaluate side-chains 73 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 115 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.081844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.055022 restraints weight = 41745.726| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.77 r_work: 0.2706 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17165 Z= 0.177 Angle : 0.600 8.347 23495 Z= 0.296 Chirality : 0.045 0.137 2755 Planarity : 0.004 0.033 2840 Dihedral : 4.967 25.882 2645 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.46 % Allowed : 11.60 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.20), residues: 1955 helix: 2.52 (0.19), residues: 790 sheet: -0.06 (0.26), residues: 330 loop : -0.78 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 320 HIS 0.004 0.001 HIS C 119 PHE 0.016 0.001 PHE C 233 TYR 0.025 0.002 TYR A 116 ARG 0.010 0.000 ARG E 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00289 ( 15) link_NAG-ASN : angle 3.51989 ( 45) hydrogen bonds : bond 0.05410 ( 840) hydrogen bonds : angle 4.12156 ( 2610) SS BOND : bond 0.00540 ( 5) SS BOND : angle 0.89078 ( 10) covalent geometry : bond 0.00421 (17145) covalent geometry : angle 0.58052 (23440) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 71 time to evaluate : 1.831 Fit side-chains REVERT: A 235 MET cc_start: 0.8642 (tpp) cc_final: 0.8026 (mpp) REVERT: A 267 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8531 (tp) REVERT: B 267 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8669 (tp) REVERT: C 267 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8572 (tp) REVERT: D 267 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8664 (tp) REVERT: E 267 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8515 (tp) outliers start: 27 outliers final: 10 residues processed: 97 average time/residue: 0.9306 time to fit residues: 106.5298 Evaluate side-chains 77 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 317 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 188 optimal weight: 8.9990 chunk 17 optimal weight: 0.4980 chunk 75 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 10 optimal weight: 0.0470 chunk 79 optimal weight: 4.9990 chunk 172 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.083778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.057027 restraints weight = 41559.222| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.78 r_work: 0.2751 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17165 Z= 0.103 Angle : 0.530 9.451 23495 Z= 0.257 Chirality : 0.042 0.127 2755 Planarity : 0.003 0.031 2840 Dihedral : 4.456 25.226 2645 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.76 % Allowed : 13.39 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.20), residues: 1955 helix: 2.61 (0.19), residues: 800 sheet: -0.07 (0.26), residues: 330 loop : -0.77 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 320 HIS 0.002 0.001 HIS E 323 PHE 0.007 0.001 PHE A 242 TYR 0.011 0.001 TYR E 67 ARG 0.006 0.000 ARG A 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 15) link_NAG-ASN : angle 2.63323 ( 45) hydrogen bonds : bond 0.04617 ( 840) hydrogen bonds : angle 3.85236 ( 2610) SS BOND : bond 0.00279 ( 5) SS BOND : angle 0.57583 ( 10) covalent geometry : bond 0.00209 (17145) covalent geometry : angle 0.51729 (23440) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 1.844 Fit side-chains REVERT: A 267 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8384 (tp) REVERT: B 182 ILE cc_start: 0.6591 (mm) cc_final: 0.6295 (mt) REVERT: B 267 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8628 (tp) REVERT: C 267 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8480 (tp) REVERT: D 182 ILE cc_start: 0.6934 (mm) cc_final: 0.6698 (mt) REVERT: D 267 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8577 (tp) REVERT: E 182 ILE cc_start: 0.7077 (mm) cc_final: 0.6705 (mt) REVERT: E 267 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8466 (tp) outliers start: 14 outliers final: 6 residues processed: 90 average time/residue: 0.9032 time to fit residues: 96.2871 Evaluate side-chains 77 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 36 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 104 optimal weight: 8.9990 chunk 131 optimal weight: 4.9990 chunk 187 optimal weight: 0.0070 chunk 152 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 overall best weight: 1.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.083091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.056336 restraints weight = 41411.818| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.77 r_work: 0.2734 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17165 Z= 0.121 Angle : 0.541 10.143 23495 Z= 0.262 Chirality : 0.042 0.128 2755 Planarity : 0.003 0.036 2840 Dihedral : 4.455 26.236 2645 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.36 % Allowed : 13.28 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.20), residues: 1955 helix: 2.67 (0.19), residues: 795 sheet: -0.05 (0.26), residues: 330 loop : -0.74 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 320 HIS 0.002 0.001 HIS E 323 PHE 0.007 0.001 PHE C 242 TYR 0.015 0.001 TYR C 67 ARG 0.010 0.000 ARG C 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00234 ( 15) link_NAG-ASN : angle 2.74467 ( 45) hydrogen bonds : bond 0.04711 ( 840) hydrogen bonds : angle 3.85475 ( 2610) SS BOND : bond 0.00357 ( 5) SS BOND : angle 0.71615 ( 10) covalent geometry : bond 0.00271 (17145) covalent geometry : angle 0.52818 (23440) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 2.069 Fit side-chains REVERT: A 267 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8408 (tp) REVERT: B 182 ILE cc_start: 0.6668 (mm) cc_final: 0.6334 (mt) REVERT: B 267 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8615 (tp) REVERT: B 291 MET cc_start: 0.8616 (mmm) cc_final: 0.8391 (mmm) REVERT: C 235 MET cc_start: 0.8909 (tpp) cc_final: 0.8245 (mpp) REVERT: C 267 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8506 (tp) REVERT: D 182 ILE cc_start: 0.6971 (mm) cc_final: 0.6734 (mt) REVERT: D 267 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8632 (tp) REVERT: E 182 ILE cc_start: 0.7052 (mm) cc_final: 0.6678 (mt) REVERT: E 267 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8477 (tp) outliers start: 25 outliers final: 8 residues processed: 91 average time/residue: 0.9025 time to fit residues: 97.0822 Evaluate side-chains 76 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 65 optimal weight: 10.0000 chunk 135 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 chunk 24 optimal weight: 0.0770 chunk 70 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.082347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.055701 restraints weight = 41234.493| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.76 r_work: 0.2722 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17165 Z= 0.135 Angle : 0.562 10.333 23495 Z= 0.271 Chirality : 0.043 0.139 2755 Planarity : 0.004 0.042 2840 Dihedral : 4.559 27.070 2645 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.03 % Allowed : 13.60 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.20), residues: 1955 helix: 2.72 (0.19), residues: 795 sheet: -0.07 (0.26), residues: 330 loop : -0.73 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 320 HIS 0.002 0.001 HIS B 323 PHE 0.008 0.001 PHE D 233 TYR 0.016 0.001 TYR B 67 ARG 0.008 0.000 ARG C 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00188 ( 15) link_NAG-ASN : angle 2.99499 ( 45) hydrogen bonds : bond 0.04904 ( 840) hydrogen bonds : angle 3.90273 ( 2610) SS BOND : bond 0.00399 ( 5) SS BOND : angle 0.76907 ( 10) covalent geometry : bond 0.00310 (17145) covalent geometry : angle 0.54677 (23440) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 1.758 Fit side-chains REVERT: A 267 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8413 (tp) REVERT: B 54 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8674 (pttm) REVERT: B 235 MET cc_start: 0.8705 (tpp) cc_final: 0.8023 (mpp) REVERT: B 267 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8657 (tp) REVERT: C 235 MET cc_start: 0.8878 (tpp) cc_final: 0.8031 (mpp) REVERT: C 267 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8537 (tp) REVERT: D 267 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8637 (tp) REVERT: E 182 ILE cc_start: 0.7138 (mm) cc_final: 0.6761 (mt) REVERT: E 235 MET cc_start: 0.8820 (tpp) cc_final: 0.7962 (mpp) REVERT: E 267 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8457 (tp) outliers start: 19 outliers final: 8 residues processed: 84 average time/residue: 0.8440 time to fit residues: 84.4897 Evaluate side-chains 77 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 68 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 85 optimal weight: 0.0000 chunk 88 optimal weight: 0.0000 chunk 87 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.083814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.057270 restraints weight = 41231.001| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.76 r_work: 0.2758 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17165 Z= 0.103 Angle : 0.533 11.598 23495 Z= 0.257 Chirality : 0.042 0.143 2755 Planarity : 0.003 0.046 2840 Dihedral : 4.312 26.524 2645 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.87 % Allowed : 14.09 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.20), residues: 1955 helix: 2.68 (0.19), residues: 800 sheet: -0.06 (0.26), residues: 330 loop : -0.69 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP E 320 HIS 0.002 0.000 HIS B 309 PHE 0.007 0.001 PHE D 233 TYR 0.011 0.001 TYR A 286 ARG 0.006 0.000 ARG C 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00336 ( 15) link_NAG-ASN : angle 2.45239 ( 45) hydrogen bonds : bond 0.04459 ( 840) hydrogen bonds : angle 3.74129 ( 2610) SS BOND : bond 0.00242 ( 5) SS BOND : angle 0.58169 ( 10) covalent geometry : bond 0.00208 (17145) covalent geometry : angle 0.52277 (23440) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 2.046 Fit side-chains REVERT: A 267 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8373 (tp) REVERT: B 54 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8680 (pttm) REVERT: B 182 ILE cc_start: 0.6685 (mm) cc_final: 0.6388 (mt) REVERT: B 235 MET cc_start: 0.8722 (tpp) cc_final: 0.8069 (mpp) REVERT: B 267 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8593 (tp) REVERT: C 235 MET cc_start: 0.8851 (tpp) cc_final: 0.8000 (mpp) REVERT: C 267 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8493 (tp) REVERT: D 182 ILE cc_start: 0.6993 (mm) cc_final: 0.6739 (mt) REVERT: D 267 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8569 (tp) REVERT: E 182 ILE cc_start: 0.7096 (mm) cc_final: 0.6715 (mt) REVERT: E 267 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8440 (tp) outliers start: 16 outliers final: 7 residues processed: 85 average time/residue: 0.9806 time to fit residues: 98.1828 Evaluate side-chains 77 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 193 optimal weight: 1.9990 chunk 85 optimal weight: 0.2980 chunk 153 optimal weight: 6.9990 chunk 119 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 120 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 148 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.083658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.057036 restraints weight = 41345.144| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.76 r_work: 0.2752 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17165 Z= 0.106 Angle : 0.547 10.566 23495 Z= 0.262 Chirality : 0.042 0.151 2755 Planarity : 0.004 0.047 2840 Dihedral : 4.309 27.125 2645 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.81 % Allowed : 14.63 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.20), residues: 1955 helix: 2.70 (0.19), residues: 800 sheet: -0.02 (0.26), residues: 330 loop : -0.67 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP E 320 HIS 0.002 0.001 HIS D 323 PHE 0.007 0.001 PHE D 233 TYR 0.012 0.001 TYR C 67 ARG 0.011 0.000 ARG B 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00273 ( 15) link_NAG-ASN : angle 2.47058 ( 45) hydrogen bonds : bond 0.04439 ( 840) hydrogen bonds : angle 3.72810 ( 2610) SS BOND : bond 0.00258 ( 5) SS BOND : angle 0.65891 ( 10) covalent geometry : bond 0.00225 (17145) covalent geometry : angle 0.53666 (23440) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 1.955 Fit side-chains REVERT: A 267 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8365 (tp) REVERT: B 54 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8679 (pttm) REVERT: B 182 ILE cc_start: 0.6647 (mm) cc_final: 0.6346 (mt) REVERT: B 235 MET cc_start: 0.8738 (tpp) cc_final: 0.8105 (mpp) REVERT: B 267 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8609 (tp) REVERT: C 235 MET cc_start: 0.8848 (tpp) cc_final: 0.8002 (mpp) REVERT: C 267 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8496 (tp) REVERT: D 182 ILE cc_start: 0.6971 (mm) cc_final: 0.6723 (mt) REVERT: D 267 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8563 (tp) REVERT: E 182 ILE cc_start: 0.7107 (mm) cc_final: 0.6735 (mt) REVERT: E 267 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8433 (tp) outliers start: 15 outliers final: 8 residues processed: 76 average time/residue: 0.8439 time to fit residues: 77.2664 Evaluate side-chains 77 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 137 optimal weight: 0.9990 chunk 176 optimal weight: 0.0870 chunk 138 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 34 optimal weight: 0.3980 chunk 158 optimal weight: 1.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.084043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.057447 restraints weight = 41452.255| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.76 r_work: 0.2761 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17165 Z= 0.103 Angle : 0.541 12.233 23495 Z= 0.259 Chirality : 0.042 0.148 2755 Planarity : 0.004 0.050 2840 Dihedral : 4.244 27.311 2645 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.92 % Allowed : 14.58 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.20), residues: 1955 helix: 2.70 (0.19), residues: 800 sheet: -0.00 (0.26), residues: 330 loop : -0.65 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP D 320 HIS 0.002 0.000 HIS D 323 PHE 0.008 0.001 PHE D 233 TYR 0.012 0.001 TYR C 67 ARG 0.009 0.000 ARG B 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00289 ( 15) link_NAG-ASN : angle 2.39415 ( 45) hydrogen bonds : bond 0.04302 ( 840) hydrogen bonds : angle 3.68230 ( 2610) SS BOND : bond 0.00232 ( 5) SS BOND : angle 0.61583 ( 10) covalent geometry : bond 0.00216 (17145) covalent geometry : angle 0.53122 (23440) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8122.35 seconds wall clock time: 139 minutes 46.29 seconds (8386.29 seconds total)